rs371047262
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr17-31232043-ATTTTTTTTTTTTTTT-A
- chr17-31232043-ATTTTTTTTTTTTTTT-AT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- chr17-31232043-ATTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001042492.3(NF1):c.3198-18_3198-4delTTTTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000022 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000036 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
NF1
NM_001042492.3 splice_region, intron
NM_001042492.3 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.14
Publications
2 publications found
Genes affected
NF1 (HGNC:7765): (neurofibromin 1) This gene product appears to function as a negative regulator of the ras signal transduction pathway. Mutations in this gene have been linked to neurofibromatosis type 1, juvenile myelomonocytic leukemia and Watson syndrome. The mRNA for this gene is subject to RNA editing (CGA>UGA->Arg1306Term) resulting in premature translation termination. Alternatively spliced transcript variants encoding different isoforms have also been described for this gene. [provided by RefSeq, Jul 2008]
NF1 Gene-Disease associations (from GenCC):
- neurofibromatosis type 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp
- neurofibromatosis-Noonan syndromeInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp
- Moyamoya diseaseInheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
- hereditary pheochromocytoma-paragangliomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- familial ovarian cancerInheritance: Unknown Classification: NO_KNOWN Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
BP6
Variant 17-31232043-ATTTTTTTTTTTTTTT-A is Benign according to our data. Variant chr17-31232043-ATTTTTTTTTTTTTTT-A is described in ClinVar as Likely_benign. ClinVar VariationId is 3878983.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001042492.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NF1 | TSL:1 MANE Select | c.3198-29_3198-15delTTTTTTTTTTTTTTT | intron | N/A | ENSP00000351015.4 | P21359-1 | |||
| NF1 | TSL:1 | c.3198-29_3198-15delTTTTTTTTTTTTTTT | intron | N/A | ENSP00000348498.3 | P21359-2 | |||
| NF1 | TSL:1 | n.3198-29_3198-15delTTTTTTTTTTTTTTT | intron | N/A | ENSP00000462408.2 | J3KSB5 |
Frequencies
GnomAD3 genomes 0.0000220 AC: 2AN: 90908Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
90908
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000361 AC: 18AN: 499014Hom.: 1 AF XY: 0.0000419 AC XY: 11AN XY: 262428 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
18
AN:
499014
Hom.:
AF XY:
AC XY:
11
AN XY:
262428
show subpopulations
African (AFR)
AF:
AC:
0
AN:
10162
American (AMR)
AF:
AC:
0
AN:
16036
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
12226
East Asian (EAS)
AF:
AC:
0
AN:
16806
South Asian (SAS)
AF:
AC:
0
AN:
42948
European-Finnish (FIN)
AF:
AC:
14
AN:
28846
Middle Eastern (MID)
AF:
AC:
0
AN:
1682
European-Non Finnish (NFE)
AF:
AC:
4
AN:
348460
Other (OTH)
AF:
AC:
0
AN:
21848
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
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55-60
60-65
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>80
Age
GnomAD4 genome 0.0000220 AC: 2AN: 90908Hom.: 0 Cov.: 0 AF XY: 0.0000238 AC XY: 1AN XY: 42040 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
90908
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
42040
show subpopulations
African (AFR)
AF:
AC:
0
AN:
22426
American (AMR)
AF:
AC:
0
AN:
7422
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2612
East Asian (EAS)
AF:
AC:
0
AN:
2728
South Asian (SAS)
AF:
AC:
0
AN:
2360
European-Finnish (FIN)
AF:
AC:
2
AN:
3380
Middle Eastern (MID)
AF:
AC:
0
AN:
196
European-Non Finnish (NFE)
AF:
AC:
0
AN:
47886
Other (OTH)
AF:
AC:
0
AN:
1220
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.725
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Hereditary cancer-predisposing syndrome;CN230736:Cardiovascular phenotype (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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